Synthetic Approaches to Studying Cis-Regulation

Synthetic Approaches to Studying Cis-Regulation

Abstract:

Next-generation sequencing technologies have enabled simple genome-wide measurements of a variety of biological processes. Consortiums like ENCODE seek to identify all functional DNA elements in humans and other model organisms by correlating functional outputs with sequence using genome-wide data sets. However, proving that particular sequences have causative effects on gene expression requires carefully controlled transgene expression or gene editing studies. Conducting such experiments on genome-wide scales is difficult because of our inability to (1) rapidly alter the sequence and context of individual genetic elements and (2) quantify the consequences of thousands of such changes.
In this talk, I will discuss our efforts to bring our DNA synthesis capacities to genomic scales in order to systematically test hypotheses of cis-regulatory control. First, we have leveraged DNA microarrays to assemble gene-sized constructs to both lower costs and increase scales of gene synthesis. Second, we developed methods to characterize large libraries of synthetic DNA in multiplex using next-generation sequencing. We synthesized ~27,000 combinations of promoter, ribosome binding site, and peptide leader sequences in an effort to look at the composability of regulatory elements governing gene expression in E. coli. We are able to quantify both the transcription and translation levels of each member of the library independently, leading to insights on how regulatory elements in combination affect transcription and translation rates. Finally, I will discuss our ongoing and future efforts of both increasing scale of DNA syntheses and applying these methodologies to human cell lines.

Bio:

Kosuri is developing next-generation DNA synthesis technologies for use in bioengineering. As a Wyss Postdoctoral Fellow, he conducted research on multiplexed and automated genome engineering and DNA synthesis technologies for two years before moving to the Advanced Technology Team. Prior to the Wyss, Kosuri was a Senior Scientist and the first employee at Joule Unlimited, a biofuel startup company that uses engineered cyanobacteria to convert light directly into renewable fuels and chemical compounds. He has authored several patents and patent applications related to both biofuels and DNA synthesis technologies. Kosuri received his B.S. in Bioengineering from the University of California, Berkeley, in 2001 and his Sc.D. in Biological Engineering from the Massachusetts Institute of Technology in 2007.